SC Controls RNA-Seq

All samples

Reduced dimensionality representation

PCA (group)

PCA Tools

## -- removing the lower 10% of variables based on variance
## -- variables retained:
## Gm26825, Ldhc, RP23-79J21.2, Rpl15-ps3, n-R5s100, AC164158.1, RP23-8J15.3, Agpat2, St14, RP24-333C3.5, Obscn

SessionInfo

## ─ Session info ──────────────────────────────────────────────────────────
##  setting  value                       
##  version  R version 3.5.3 (2019-03-11)
##  os       Ubuntu 16.04.6 LTS          
##  system   x86_64, linux-gnu           
##  ui       X11                         
##  language (EN)                        
##  collate  en_US.UTF-8                 
##  ctype    en_US.UTF-8                 
##  tz       Europe/Zurich               
##  date     2019-06-18                  
## 
## ─ Packages ──────────────────────────────────────────────────────────────
##  package              * version   date       lib
##  acepack                1.4.1     2016-10-29 [1]
##  annotate               1.60.1    2019-03-07 [1]
##  AnnotationDbi          1.44.0    2018-10-30 [1]
##  assertthat             0.2.1     2019-03-21 [1]
##  autoplotly           * 0.1.2     2018-04-21 [1]
##  backports              1.1.4     2019-04-10 [1]
##  base64enc              0.1-3     2015-07-28 [1]
##  Biobase                2.42.0    2018-10-30 [1]
##  BiocGenerics           0.28.0    2018-10-30 [1]
##  BiocParallel           1.16.6    2019-02-10 [1]
##  Biostrings             2.50.2    2019-01-03 [1]
##  bit                    1.1-14    2018-05-29 [1]
##  bit64                  0.9-7     2017-05-08 [1]
##  bitops                 1.0-6     2013-08-17 [1]
##  blob                   1.1.1     2018-03-25 [1]
##  bookdown               0.11      2019-05-28 [1]
##  Cairo                  1.5-10    2019-03-28 [1]
##  callr                  3.2.0     2019-03-15 [1]
##  checkmate              1.9.3     2019-05-03 [1]
##  cli                    1.1.0     2019-03-19 [1]
##  cluster                2.0.9     2019-05-01 [1]
##  colorspace             1.4-1     2019-03-18 [1]
##  corrplot             * 0.84      2017-10-16 [1]
##  cowplot              * 0.9.4     2019-01-08 [1]
##  crayon                 1.3.4     2017-09-16 [1]
##  crosstalk              1.0.0     2016-12-21 [1]
##  data.table             1.12.2    2019-04-07 [1]
##  DBI                    1.0.0     2018-05-02 [1]
##  DelayedArray           0.8.0     2018-10-30 [1]
##  dendextend           * 1.12.0    2019-05-11 [1]
##  desc                   1.2.0     2018-05-01 [1]
##  DESeq2                 1.22.2    2019-01-04 [1]
##  devtools             * 2.0.2     2019-04-08 [1]
##  digest                 0.6.19    2019-05-20 [1]
##  dplyr                  0.8.1     2019-05-14 [1]
##  edgeR                  3.24.3    2019-01-02 [1]
##  evaluate               0.14      2019-05-28 [1]
##  foreign                0.8-71    2018-07-20 [1]
##  Formula                1.2-3     2018-05-03 [1]
##  fs                     1.3.1     2019-05-06 [1]
##  genefilter             1.64.0    2018-10-30 [1]
##  geneplotter            1.60.0    2018-10-30 [1]
##  GenomeInfoDb           1.18.2    2019-02-12 [1]
##  GenomeInfoDbData       1.2.0     2019-01-17 [1]
##  GenomicRanges          1.34.0    2018-10-30 [1]
##  GEOquery               2.50.5    2018-12-22 [1]
##  ggfortify            * 0.4.7     2019-05-26 [1]
##  ggplot2              * 3.1.1     2019-04-07 [1]
##  ggplotify            * 0.0.3     2018-08-03 [1]
##  ggrepel              * 0.8.1     2019-05-07 [1]
##  glue                   1.3.1     2019-03-12 [1]
##  gridExtra              2.3       2017-09-09 [1]
##  gridGraphics           0.4-1     2019-05-20 [1]
##  gtable                 0.3.0     2019-03-25 [1]
##  highr                  0.8       2019-03-20 [1]
##  Hmisc                  4.2-0     2019-01-26 [1]
##  hms                    0.4.2     2018-03-10 [1]
##  htmlTable              1.13.1    2019-01-07 [1]
##  htmltools              0.3.6     2017-04-28 [1]
##  htmlwidgets            1.3       2018-09-30 [1]
##  httpuv                 1.5.1     2019-04-05 [1]
##  httr                   1.4.0     2018-12-11 [1]
##  IRanges                2.16.0    2018-10-30 [1]
##  jsonlite               1.6       2018-12-07 [1]
##  knitr                  1.23      2019-05-18 [1]
##  labeling               0.3       2014-08-23 [1]
##  later                  0.8.0     2019-02-11 [1]
##  lattice              * 0.20-38   2018-11-04 [1]
##  latticeExtra           0.6-28    2016-02-09 [1]
##  lazyeval               0.2.2     2019-03-15 [1]
##  limma                * 3.38.3    2018-12-02 [1]
##  locfit                 1.5-9.1   2013-04-20 [1]
##  magrittr               1.5       2014-11-22 [1]
##  Matrix                 1.2-17    2019-03-22 [1]
##  matrixStats            0.54.0    2018-07-23 [1]
##  memoise                1.1.0     2017-04-21 [1]
##  mime                   0.7       2019-06-11 [1]
##  miniUI                 0.1.1.1   2018-05-18 [1]
##  munsell                0.5.0     2018-06-12 [1]
##  nnet                   7.3-12    2016-02-02 [1]
##  PCAtools             * 0.99.13   2019-06-18 [1]
##  pheatmap             * 1.0.12    2019-01-04 [1]
##  pillar                 1.4.1     2019-05-28 [1]
##  pkgbuild               1.0.3     2019-03-20 [1]
##  pkgconfig              2.0.2     2018-08-16 [1]
##  pkgload                1.0.2     2018-10-29 [1]
##  plgINS               * 0.1.5     2019-06-07 [1]
##  plotly               * 4.9.0     2019-04-10 [1]
##  plyr                   1.8.4     2016-06-08 [1]
##  prettyunits            1.0.2     2015-07-13 [1]
##  processx               3.3.1     2019-05-08 [1]
##  promises               1.0.1     2018-04-13 [1]
##  ps                     1.3.0     2018-12-21 [1]
##  purrr                  0.3.2     2019-03-15 [1]
##  questionr              0.7.0     2018-11-26 [1]
##  R6                     2.4.0     2019-02-14 [1]
##  RColorBrewer         * 1.1-2     2014-12-07 [1]
##  Rcpp                   1.0.1     2019-03-17 [1]
##  RCurl                  1.95-4.12 2019-03-04 [1]
##  readr                  1.3.1     2018-12-21 [1]
##  remotes                2.0.4     2019-04-10 [1]
##  reshape2             * 1.4.3     2017-12-11 [1]
##  rlang                  0.3.4     2019-04-07 [1]
##  rmarkdown              1.13      2019-05-22 [1]
##  rmdformats             0.3.5     2019-02-19 [1]
##  rpart                  4.1-15    2019-04-12 [1]
##  rprojroot              1.3-2     2018-01-03 [1]
##  RSQLite                2.1.1     2018-05-06 [1]
##  rstudioapi             0.10      2019-03-19 [1]
##  rvcheck                0.1.3     2018-12-06 [1]
##  S4Vectors              0.20.1    2018-11-09 [1]
##  scales                 1.0.0     2018-08-09 [1]
##  sessioninfo            1.1.1     2018-11-05 [1]
##  shiny                  1.3.2     2019-04-22 [1]
##  SRAdb                  1.44.0    2018-10-30 [1]
##  stringi                1.4.3     2019-03-12 [1]
##  stringr                1.4.0     2019-02-10 [1]
##  SummarizedExperiment   1.12.0    2018-10-30 [1]
##  survival               2.44-1.1  2019-04-01 [1]
##  testthat               2.1.1     2019-04-23 [1]
##  tibble                 2.1.3     2019-06-06 [1]
##  tidyr                  0.8.3     2019-03-01 [1]
##  tidyselect             0.2.5     2018-10-11 [1]
##  usethis              * 1.5.0     2019-04-07 [1]
##  viridis              * 0.5.1     2018-03-29 [1]
##  viridisLite          * 0.3.0     2018-02-01 [1]
##  withr                  2.1.2     2018-03-15 [1]
##  xfun                   0.7       2019-05-14 [1]
##  XML                    3.98-1.20 2019-06-06 [1]
##  xml2                   1.2.0     2018-01-24 [1]
##  xtable                 1.8-4     2019-04-21 [1]
##  XVector                0.22.0    2018-10-30 [1]
##  yaml                   2.2.0     2018-07-25 [1]
##  zlibbioc               1.28.0    2018-10-30 [1]
##  source                               
##  CRAN (R 3.5.1)                       
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##  CRAN (R 3.5.1)                       
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##  Bioconductor                         
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##  Bioconductor                         
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##  Bioconductor                         
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##  Bioconductor                         
##  Bioconductor                         
##  Bioconductor                         
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##  CRAN (R 3.5.1)                       
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##  CRAN (R 3.5.1)                       
##  Bioconductor                         
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##  CRAN (R 3.5.1)                       
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##  Bioconductor                         
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##  CRAN (R 3.5.1)                       
##  CRAN (R 3.5.1)                       
##  Github (kevinblighe/PCAtools@3899b65)
##  CRAN (R 3.5.2)                       
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##  local                                
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##  CRAN (R 3.5.1)                       
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##  CRAN (R 3.5.1)                       
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##  Bioconductor                         
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##  CRAN (R 3.5.2)                       
##  Bioconductor                         
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##  CRAN (R 3.5.3)                       
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##  CRAN (R 3.5.2)                       
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##  CRAN (R 3.5.1)                       
##  CRAN (R 3.5.1)                       
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##  CRAN (R 3.5.3)                       
##  CRAN (R 3.5.3)                       
##  CRAN (R 3.5.1)                       
##  CRAN (R 3.5.3)                       
##  Bioconductor                         
##  CRAN (R 3.5.1)                       
##  Bioconductor                         
## 
## [1] /home/ubuntu/R/x86_64-pc-linux-gnu-library/3.5
## [2] /usr/local/lib/R/site-library
## [3] /usr/lib/R/site-library
## [4] /usr/lib/R/library

Deepak Tanwar

Created on: 2019-06-18
Updated on: 2019-06-18